Tables for
Volume F
Crystallography of biological macromolecules
Edited by M. G. Rossmann and E. Arnold

International Tables for Crystallography (2006). Vol. F, ch. 25.2, pp. 695-743

Chapter 25.2. Programs and program systems in wide use

W. Furey,a K. D. Cowtan,b K. Y. J. Zhang,c P. Main,d A. T. Brunger,v P. D. Adams,e W. L. DeLano,f P. Gros,g R. W. Grosse-Kunstleve,e J.-S. Jiang,h N. S. Pannu,i R. J. Read,j L. M. Rice,k T. Simonson,l D. E. Tronrud,m L. F. Ten Eyck,y V. S. Lamzin,n A. Perrakis,o K. S. Wilson,p R. A. Laskowski,w M. W. MacArthur,q J. M. Thornton,x P. J. Kraulis,r D. C. Richardson,s J. S. Richardson,s W. Kabscht and G. M. Sheldricku

aBiocrystallography Laboratory, VA Medical Center, PO Box 12055, University Drive C, Pittsburgh, PA 15240, USA, and Department of Pharmacology, University of Pittsburgh School of Medicine, 1340 BSTWR, Pittsburgh, PA 15261, USA,bDepartment of Chemistry, University of York, York YO1 5DD, England,cDivision of Basic Sciences, Fred Hutchinson Cancer Research Center, 1100 Fairview Ave N., Seattle, WA 90109, USA,dDepartment of Physics, University of York, York YO1 5DD, England,eThe Howard Hughes Medical Institute and Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT 06511, USA,fGraduate Group in Biophysics, Box 0448, University of California, San Francisco, CA 94143, USA,gCrystal and Structural Chemistry, Bijvoet Center for Biomolecular Research, Utrecht University, Padualaan 8, 3584 CH Utrecht, The Netherlands,hProtein Data Bank, Biology Department, Brookhaven National Laboratory, Upton, NY 11973-5000, USA,iDepartment of Mathematical Sciences, University of Alberta, Edmonton, Alberta, Canada T6G 2G1,jDepartment of Haematology, University of Cambridge, Wellcome Trust Centre for Molecular Mechanisms in Disease, CIMR, Wellcome Trust/MRC Building, Hills Road, Cambridge CB2 2XY, England,kDepartment of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT 06511, USA,lLaboratoire de Biologie Structurale (CNRS), IGBMC, 1 rue Laurent Fries, 67404 Illkirch (CU de Strasbourg), France,mHoward Hughes Medical Institute, Institute of Molecular Biology, 1229 University of Oregon, Eugene, OR 97403-1229, USA,nEuropean Molecular Biology Laboratory (EMBL), Hamburg Outstation, c/o DESY, Notkestr. 85, 22603 Hamburg, Germany,oEuropean Molecular Biology Laboratory (EMBL), Grenoble Outstation, c/o ILL, Avenue des Martyrs, BP 156, 38042 Grenoble CEDEX 9, France,pStructural Biology Laboratory, Department of Chemistry, University of York, Heslington, York YO10 5DD, England,qBiochemistry and Molecular Biology Department, University College London, Gower Street, London WC1E 6BT, England,rStockholm Bioinformatics Center, Department of Biochemistry, Stockholm University, SE-106 91 Stockholm, Sweden,sDepartment of Biochemistry, Duke University Medical Center, Durham, NC 27710-3711, USA,tMax-Planck-Institut für medizinische Forschung, Abteilung Biophysik, Jahnstrasse 29, 69120 Heidelberg, Germany,uLehrstuhl für Strukturchemie, Universität Göttingen, Tammannstrasse 4, D-37077 Göttingen, Germany,vHoward Hughes Medical Institute, and Departments of Molecular and Cellular Physiology, Neurology and Neurological Sciences, and Stanford Synchrotron Radiation Laboratory (SSRL), Stanford University, 1201 Welch Road, MSLS P210, Stanford, CA 94305, USA,wDepartment of Crystallography, Birkbeck College, University of London, Malet Street, London WC1E 7HX, England,xBiochemistry and Molecular Biology Department, University College London, Gower Street, London WC1E 6BT, England, and Department of Crystallography, Birkbeck College, University of London, Malet Street, London WC1E 7HX, England, and ySan Diego Supercomputer Center 0505, University of California at San Diego, 9500 Gilman Drive, La Jolla, CA 92093-0505, USA


Abrahams, J. P. (1993). Compression of X-ray images. Jt CCP4 ESF–EACBM Newsl. Protein Crystallogr. 28, 3–4.Google Scholar
Abrahams, J. P. (1996). Likelihood-weighted real space restraints for refinement at low resolution. In Proceedings of the CCP4 study weekend. Macromolecular refinement, edited by E. Dodson, M. Moore, A. Ralph & S. Bailey. Warrington: Daresbury Laboratory.Google Scholar
Abrahams, J. P. (1997). Bias reduction in phase refinement by modified interference functions: introducing the γ correction. Acta Cryst. D53, 371–376.Google Scholar
Abrahams, J. P. & Leslie, A. G. W. (1996). Methods used in the structure determination of bovine mitochondrial F2 ATPase. Acta Cryst. D52, 30–42.Google Scholar
Adams, P. D., Pannu, N. S., Read, R. J. & Brünger, A. T. (1997). Cross-validated maximum likelihood enhances crystallographic simulated annealing refinement. Proc. Natl Acad. Sci. USA, 94, 5018–5023.Google Scholar
Adobe Systems Inc. (1985). PostScript language reference manual. Reading, MA: Addison-Wesley.Google Scholar
Agarwal, R. C. (1978). A new least-squares technique based on the fast Fourier transform algorithm. Acta Cryst. A34, 791–809.Google Scholar
Agarwal, R. C., Lifchitz, A. & Dodson, E. (1981). Block diagonal least squares refinement using fast Fourier techniques. In Refinement of protein structures, edited by P. A. Machin, J. W. Campbell & M. Elder. Warrington: Daresbury Laboratory.Google Scholar
Allen, F. H., Bellard, S., Brice, M. D., Cartwright, B. A., Doubleday, A., Higgs, H., Hummelink, T., Hummelink-Peters, B. G., Kennard, O., Motherwell, W. D. S., Rodgers, J. R. & Watson, D. G. (1979). The Cambridge Crystallographic Data Centre: computer-based search, retrieval, analysis and display of information. Acta Cryst. B35, 2331–2339.Google Scholar
Axelsson, O. & Barker, V. (1984). Finite element solution of boundary value problems, ch. 1, pp. 1–63. Orlando: Academic Press.Google Scholar
Bateman, R. C. (2000). Undergraduate kinemage authorship homepage.∼rbateman/kinemage/ .Google Scholar
Bernstein, F. C., Koetzle, T. F., Williams, G. J. B., Meyer, E. F. Jr, Brice, M. D., Rodgers, J. R., Kennard, O., Shimanouchi, T. & Tasumi, M. (1977). The Protein Data Bank: a computer-based archival file for macromolecular structures. J. Mol. Biol. 112, 535–542.Google Scholar
Blow, D. M. & Crick, F. H. C. (1959). The treatment of errors in the isomorphous replacement method. Acta Cryst. 12, 794–802.Google Scholar
Blundell, T. L. & Johnson, L. N. (1976). Protein crystallography, pp. 375–377. London: Academic Press.Google Scholar
Bolin, J. T., Smith, J. L. & Muchmore, S. W. (1993). Considerations in phase refinement and extension: experiments with a rapid and automatic procedure. Am. Crystallogr. Assoc. Meet. Abstracts, Vol. 21, V001, 51.Google Scholar
Bricogne, G. (1974). Geometric sources of redundancy in intensity data and their use for phase determination. Acta Cryst. A30, 395–405.Google Scholar
Bricogne, G. (1976). Methods and programs for direct-space exploitation of geometric redundancies. Acta Cryst. A32, 832–846.Google Scholar
Bricogne, G. (1984). Maximum entropy and the foundations of direct methods. Acta Cryst. A40, 410–445.Google Scholar
Bricogne, G. (1991). A multisolution method of phase determination by combined maximization of entropy and likelihood. III. Extension to powder diffraction data. Acta Cryst. A47, 803–829.Google Scholar
Bricogne, G. & Irwin, J. J. (1996). Maximum-likelihood refinement of incomplete models with BUSTER–TNT. In Proceedings of the macromolecular crystallographic computing school, edited by P. Bourne & K. Watenpaugh. .Google Scholar
Brünger, A. T. (1988). Crystallographic refinement by simulated annealing: application to a 2.8 Å resolution structure of aspartate aminotransferase. J. Mol. Biol. 203, 803–816.Google Scholar
Brünger, A. T. (1992a). X-PLOR. Version 3.1. A system for X-ray crystallography and NMR. Yale University Press, New Haven.Google Scholar
Brünger, A. T. (1992b). Free R value: a novel statistical quantity for assessing the accuracy of crystal structures. Nature (London), 355, 472–475.Google Scholar
Brünger, A. T., Adams, P. D., Clore, G. M., DeLano, W. L., Gros, P., Grosse-Kunstleve, R. W., Jiang, J.-S., Kuszewski, J., Nilges, M., Pannu, N. S., Read, R. J., Rice, L. M., Simonson, T. & Warren, G. L. (1998). Crystallography & NMR System (CNS): a new software suite for macromolecular structure determination. Acta Cryst. D54, 905–921.Google Scholar
Brünger, A. T., Adams, P. D. & Rice, L. M. (1997). New applications of simulated annealing in X-ray crystallography and solution NMR. Structure, 5, 325–336. Google Scholar
Brünger, A. T., Karplus, M. & Petsko, G. A. (1989). Crystallographic refinement by simulated annealing: application to crambin. Acta Cryst. A45, 50–61.Google Scholar
Brünger, A. T., Krukowski, A. & Erickson, J. W. (1990). Slow-cooling protocols for crystallographic refinement by simulated annealing. Acta Cryst. A46, 585–593.Google Scholar
Brünger, A. T., Kuriyan, J. & Karplus, M. (1987). Crystallographic R factor refinement by molecular dynamics. Science, 235, 458–460.Google Scholar
Buerger, M. J. (1959). Vector space and its application in crystal structure investigation. New York: Wiley.Google Scholar
Buerger, M. J. (1964). Image methods in crystal structure analysis. In Advanced methods of crystallography, edited by G. N. Ramachandran, pp. 1–24. Orlando, Florida: Academic Press.Google Scholar
Burling, F. T. & Brünger, A. T. (1994). Thermal motion and conformational disorder in protein crystal structures: comparison of multi-conformer and time-averaging models. Isr. J. Chem. 34, 165–175.Google Scholar
Burling, F. T., Weis, W. I., Flaherty, K. M. & Brünger, A. T. (1996). Direct observation of protein solvation and discrete disorder with experimental crystallographic phases. Science, 271, 72–77.Google Scholar
Busetta, B., Giacovazzo, C., Burla, M. C., Nunzi, A., Polidori, G. & Viterbo, D. (1980). The SIR program. I. Use of negative quartets. Acta Cryst. A36, 68–74.Google Scholar
Chapman, M. S., Tsao, J. & Rossmann, M. G. (1992). Ab initio phase determination for spherical viruses: parameter determination for spherical-shell models. Acta Cryst. A48, 301–312.Google Scholar
Collaborative Computational Project, Number 4 (1994). The CCP4 suite: programs for protein crystallography. Acta Cryst. D50, 760–763.Google Scholar
Cowtan, K. D. & Main, P. (1996). Phase combination and cross validation in iterated density-modification calculations. Acta Cryst. D52, 43–48.Google Scholar
Cowtan, K. D. & Main, P. (1998). Miscellaneous algorithms for density modification. Acta Cryst. D54, 487–493.Google Scholar
Cruickshank, D. W. J. (1970). Least-squares refinement of atomic parameters. In Crystallographic computing, edited by F. R. Ahmed, S. R. Hall & C. P. Huber, pp. 187–197. Copenhagen: Munksgaard.Google Scholar
Dauter, Z., Lamzin, V. S. & Wilson, K. S. (1997). The benefits of atomic resolution. Curr. Opin. Struct. Biol. 7, 681–688.Google Scholar
Debaerdemaeker, T., Tate, C. & Woolfson, M. M. (1985). On the application of phase relationships to complex structures. XXIV. The Sayre tangent formula. Acta Cryst. A41, 286–290.Google Scholar
Diederichs, K. & Karplus, P. A. (1997). Improved R-factors for diffraction data analysis in macromolecular crystallography. Nature Struct. Biol. 4, 269–274.Google Scholar
Eisenberg, D., Lüthy, R. & Bowie, J. U. (1997). VERIFY3D: assessment of protein models with three-dimensional profiles. Methods Enzymol. 277, 396–404.Google Scholar
Engh, R. A. & Huber, R. (1991). Accurate bond and angle parameters for X-ray protein structure refinement. Acta Cryst. A47, 392–400.Google Scholar
French, S. & Wilson, K. (1978). On the treatment of negative intensity observations. Acta Cryst. A34, 517–525.Google Scholar
Furey, W. & Swaminathan, S. (1990). PHASES – a program package for the processing and analysis of diffraction data from macromolecules. Am. Crystallogr. Assoc. Meet. Abstracts, Vol. 18, PA33, 73.Google Scholar
Furey, W. & Swaminathan, S. (1997). PHASES-95: a program package for processing and analyzing diffraction data from macromolecules. Methods Enzymol. 277, 590–620.Google Scholar
Giacovazzo, C. (2001). Direct methods. In International tables for crystallography, Vol. B. Reciprocal space, edited by U. Shmueli, ch. 2.2. Dordrecht: Kluwer Academic Publishers.Google Scholar
Graham, I. S. (1995). The HTML sourcebook. John Wiley and Sons.Google Scholar
Green, D. W., Ingram, V. M. & Perutz, M. F. (1954). The structure of haemoglobin. IV. Sign determination by the isomorphous replacement method. Proc. R. Soc. London Ser. A, 225, 287–307.Google Scholar
Greer, J. (1974). Three-dimensional pattern recognition: an approach to automated interpretation of electron density maps of proteins. J. Mol. Biol. 82, 279–301.Google Scholar
Hendrickson, W. A. (1979). Phase information from anomalous-scattering measurements. Acta Cryst. A35, 245–247.Google Scholar
Hendrickson, W. A. (1991). Determination of macromolecular structures from anomalous diffraction of synchrotron radiation. Science, 254, 51–58.Google Scholar
Hendrickson, W. A. & Konnert, J. H. (1980). Incorporation of stereochemical information into crystallographic refinement. In Computing in crystallography, edited by R. Diamond, S. Ramaseshan & K. Venkatesan, pp. 13.01–13.23. Bangalore: Indian Academy of Sciences.Google Scholar
Hendrickson, W. A. & Lattman, E. E. (1970). Representation of phase probability distributions for simplified combination of independent phase information. Acta Cryst. B26, 136–143.Google Scholar
Herbst-Irmer, R. & Sheldrick, G. M. (1998). Refinement of twinned structures with SHELXL97. Acta Cryst. B54, 443–449.Google Scholar
Hirshfeld, F. L. (1976). Can X-ray data distinguish bonding effects from vibrational smearing? Acta Cryst. A32, 239–244.Google Scholar
Holmes, M. A. & Matthews, B. W. (1981). Binding of hydroxamic acid inhibitors to crystalline thermolysin suggests a pentacoordinate zinc intermediate in catalysis. Biochemistry, 20, 6912–6920.Google Scholar
Hooft, R. W. W., Sander, C., Vriend, G. & Abola, E. E. (1996). Errors in protein structures. Nature (London), 381, 272.Google Scholar
IUPAC–IUB Commission on Biochemical Nomenclature (1970). Abbreviations and symbols for the description of the conformation of polypeptide chains. J. Mol. Biol. 52, 1–17. Google Scholar
Jack, A. & Levitt, M. (1978). Refinement of large structures by simultaneous minimization of energy and R factor. Acta Cryst. A34, 931–935.Google Scholar
Jiang, J.-S. & Brünger, A. T. (1994). Protein hydration observed by X-ray diffraction: solvation properties of penicillopepsin and neuraminidase crystal structures. J. Mol. Biol. 243, 100–115.Google Scholar
Jones, T. A. (1978). A graphics model building and refinement system for macromolecules. J. Appl. Cryst. 11, 268–272.Google Scholar
Jones, T. A., Zou, J.-Y., Cowan, S. W. & Kjeldgaard, M. (1991). Improved methods for building protein models in electron density maps and the location of errors in these models. Acta Cryst. A47, 110–119.Google Scholar
Kabsch, W. (1976). A solution for the best rotation to relate two sets of vectors. Acta Cryst. A32, 922–923.Google Scholar
Kabsch, W. (1988a). Automatic indexing of rotation diffraction patterns. J. Appl. Cryst. 21, 67–72.Google Scholar
Kabsch, W. (1988b). Evaluation of single-crystal X-ray diffraction data from a position-sensitive detector. J. Appl. Cryst. 21, 916–924.Google Scholar
Kabsch, W. (1993). Automatic processing of rotation diffraction data from crystals of initially unknown symmetry and cell constants. J. Appl. Cryst. 26, 795–800.Google Scholar
Karle, J. & Hauptman, H. (1956). A theory of phase determination for the four types of non-centrosymmetric space groups 1P222, 2P22, 3P12, 3P22. Acta Cryst. 9, 635–651.Google Scholar
Kleywegt, G. J. & Brünger, A. T. (1996). Checking your imagination: applications of the free R value. Structure, 4, 897–904.Google Scholar
Kleywegt, G. J. & Jones, T. A. (1996a). Phi/psi-chology: Ramachandran revisited. Structure, 4, 1395–1400.Google Scholar
Kleywegt, G. J. & Jones, T. A. (1996b). Efficient rebuilding of protein structures. Acta Cryst. D52, 829–832.Google Scholar
Kraulis, P. J. (1991). MOLSCRIPT: a program to produce both detailed and schematic plots of protein structures. J. Appl. Cryst. 24, 946–950.Google Scholar
Lamzin, V. S. & Wilson, K. S. (1993). Automated refinement of protein models. Acta Cryst. D49, 129–147.Google Scholar
Lamzin, V. S. & Wilson, K. S. (1997). Automated refinement for protein crystallography. Methods Enzymol. 277, 269–305.Google Scholar
Laskowski, R. A., MacArthur, M. W., Moss, D. S. & Thornton, J. M. (1993). PROCHECK: a program to check the stereochemical quality of protein structures. J. Appl. Cryst. 26, 283–291.Google Scholar
Laskowski, R. A., MacArthur, M. W. & Thornton, J. M. (1998). Validation of protein models derived from experiment. Curr. Opin. Struct. Biol. 8, 631–639.Google Scholar
Laskowski, R. A., Rullmann, J. A. C., MacArthur, M. W., Kaptein, R. & Thornton, J. M. (1996). AQUA and PROCHECK-NMR: programs for checking the quality of protein structures solved by NMR. J. Biomol. Nucl. Magn. Reson. 8, 477–486.Google Scholar
Leslie, A. G. W. (1987). A reciprocal-space method for calculating a molecular envelope using the algorithm of B. C. Wang. Acta Cryst. A43, 134–136.Google Scholar
Lewis, M. & Rees, D. C. (1983). Statistical modification of anomalous scattering differences. Acta Cryst. A39, 512–515.Google Scholar
Lovell, S. C., Word, J. M., Richardson, J. S. & Richardson, D. C. (2000). The penultimate rotamer library. Proteins Struct. Funct. Genet. 40, 389–408.Google Scholar
Luecke, H., Richter, H. T. & Lanyi, J. K. (1998). Proton transfer pathways in bacteriorhodopsin at 2.3 Å resolution. Science, 280, 1934–1937.Google Scholar
MacArthur, M. W., Laskowski, R. A. & Thornton, J. M. (1994). Knowledge-based validation of protein structure coordinates derived by X-ray crystallography and NMR spectroscopy. Curr. Opin. Struct. Biol. 4, 731–737.Google Scholar
McRee, D. E. (1992). A visual protein crystallographic software system for X11/Xview. J. Mol. Graphics, 10, 44–46.Google Scholar
McRee, D. E. (1993). Practical protein crystallography. San Diego: Academic Press.Google Scholar
McRee, D. E. (1999). XtalView/Xfit – a versatile program for manipulating atomic coordinates and electron density. J. Struct. Biol. 125, 156–165.Google Scholar
Matthews, B. W. (1968). Solvent content of protein crystals. J. Mol. Biol. 33, 491–497.Google Scholar
Matthews, B. W. (1974). Determination of molecular weight from protein crystals. J. Mol. Biol. 82, 513–526.Google Scholar
Merritt, E. A. (2000). Raster3D (photorealistic molecular graphics). .Google Scholar
Merritt, E. A. & Bacon, D. J. (1997). Raster3D: photorealistic molecular graphics. Methods Enzymol. 277, 505–525.Google Scholar
Miller, R., DeTitta, G. T., Jones, R., Langs, D. A., Weeks, C. M. & Hauptman, H. A. (1993). On the application of the minimal principle to solve unknown structures. Science, 259, 1430–1433.Google Scholar
Miller, R., Gallo, S. M., Khalak, H. G. & Weeks, C. M. (1994). SnB: crystal structure determination via Shake-and-Bake. J. Appl. Cryst. 27, 613–621.Google Scholar
Moews, P. C. & Kretsinger, R. H. (1975). Refinement of carp muscle parvalbumin by model building and difference Fourier analysis. J. Mol. Biol. 91, 201–228.Google Scholar
Morris, A. L., MacArthur, M. W., Hutchinson, E. G. & Thornton, J. M. (1992). Stereochemical quality of protein structure coordinates. Proteins, 12, 345–364.Google Scholar
MSI (1997). QUANTA. MSI, 9685 Scranton Road, San Diego, CA 92121–3752, USA. Google Scholar
Murshudov, G. N., Vagin, A. A. & Dodson, E. J. (1997). Refinement of macromolecular structures by the maximum-likelihood method. Acta Cryst. D53, 240–255.Google Scholar
Navaza, J. (1994). AMoRe: an automated package for molecular replacement. Acta Cryst. A50, 157–163.Google Scholar
Oldfield, T. J. (1992). SQUID: a program for the analysis and display of data from crystallography and molecular dynamics. J. Mol. Graphics, 10, 247–252.Google Scholar
Otwinowski, Z. (1991). In Proceedings of the CCP4 study weekend. Isomorphous replacement and anomalous scattering, edited by W. Wolf, P. R. Evans & A. G. W. Leslie, pp. 80–86. Warrington: Daresbury Laboratory.Google Scholar
Pannu, N. S., Murshudov, G. N., Dodson, E. J. & Read, R. J. (1998). Incorporation of prior phase information strengthens maximum-likelihood structure refinement. Acta Cryst. D54, 1285–1294.Google Scholar
Pannu, N. S. & Read, R. J. (1996a). Improved structure refinement through maximum likelihood. Acta Cryst. A52, 659–668.Google Scholar
Pannu, N. S. & Read, R. J. (1996b). Improved structure refinement through maximum likelihood. In Proceedings of the CCP4 study weekend. Macromolecular refinement, edited by E. Dodson, M. Moore, A. Ralph & S. Bailey. Warrington: Daresbury Laboratory.Google Scholar
Parkin, S., Moezzi, B. & Hope, H. (1995). XABS2: an empirical absorption correction program. J. Appl. Cryst. 28, 53–56.Google Scholar
Pepinsky, R. & Okaya, Y. (1956). Determination of crystal structures by means of anomalously scattered X-rays. Proc. Natl Acad. Sci. USA, 42, 286–292.Google Scholar
Perrakis, A., Morris, R. & Lamzin, V. S. (1999). Automated protein model building combined with iterative structure refinement. Nature Struct. Biol. 6, 458–463.Google Scholar
Perrakis, A., Sixma, T. K., Wilson, K. S. & Lamzin, V. S. (1997). wARP: improvement and extension of crystallographic phases by weighted averaging of multiple-refined dummy atomic models. Acta Cryst. D53, 448–455.Google Scholar
Perrakis, A., Tews, I., Dauter, Z., Oppenheim, A., Chet, I., Wilson, K. S. & Vorgias, C. E. (1994). Structure of a bacterial chitinase at 2.3 Å resolution. Structure, 2, 1169–1180.Google Scholar
Pontius, J., Richelle, J. & Wodak, S. (1996). Deviations from standard atomic volumes as a quality measure for protein crystal structures. J. Mol. Biol. 264, 121–136.Google Scholar
POV-Ray Team (2000). POV-Ray – the persistence of Vision Raytracer. .Google Scholar
Ramachandran, G. N., Ramakrishnan, C. & Sasisekharan, V. (1963). Stereochemistry of polypeptide chain configurations. J. Mol. Biol. 7, 95–99.Google Scholar
Ramakrishnan, C. & Ramachandran, G. N. (1965). Stereochemical criteria for polypeptide and protein chain conformations. II. Allowed conformations for a pair of peptide units. Biophys. J. 5, 909–933.Google Scholar
Read, R. J. (1986). Improved Fourier coefficients for maps using phases from partial structures with errors. Acta Cryst. A42, 140–149.Google Scholar
Read, R. J. (1990). Structure-factor probabilities for related structures. Acta Cryst. A46, 900–912.Google Scholar
Read, R. J. (1994). Maximum likelihood refinement of heavy atoms. Lecture notes for a workshop on isomorphous replacement methods in macromolecular crystallography. American Crystallographic Association Annual Meeting, 1994, Atlanta, GA, USA.Google Scholar
Read, R. J. (1997). Model phases: probabilities and bias. Methods Enzymol. 277, 110–128.Google Scholar
Research Collaboratory for Structural Bioinformatics (2000). The RCSB Protein Data Bank. .Google Scholar
Rice, L. M. & Brünger, A. T. (1994). Torsion angle dynamics: reduced variable conformational sampling enhances crystallographic structure refinement. Proteins Struct. Funct. Genet. 19, 277–290.Google Scholar
Richardson, D. C. & Richardson, J. S. (1992). The kinemage: a tool for scientific illustration. Protein Sci. 1, 3–9.Google Scholar
Richardson, D. C. & Richardson, J. S. (1994). Kinemages – simple macromolecular graphics for interactive teaching and publication. Trends Biochem. Sci. 19, 135–138.Google Scholar
Richardson, J. W. & Jacobson, R. A. (1987). Computer-aided analysis of multi-solution Patterson superpositions. In Patterson and Pattersons, edited by J. P. Glusker, B. Patterson & M. Rossi, pp. 311–317. Oxford: IUCr and Oxford University Press.Google Scholar
Richardson Laboratory (2000). The Richardson's 3-D protein structure homepage. (or ).Google Scholar
Rollett, J. S. (1970). Least-squares procedures in crystal structure analysis. In Crystallographic computing, edited by F. R. Ahmed, S. R. Hall & C. P. Huber, pp. 167–181. Copenhagen: Munksgaard.Google Scholar
Rossmann, M. G. & Arnold, E. (2001). Patterson and molecular-replacement techniques. In International tables for crystallography, Vol. B. Reciprocal space, edited by U. Shmueli, ch. 2.3. Dordrecht: Kluwer Academic Publishers.Google Scholar
Rossmann, M. G. & Blow, D. M. (1963). Determination of phases by the conditions of non-crystallographic symmetry. Acta Cryst. 16, 39–44.Google Scholar
Rossmann, M. G., McKenna, R., Tong, L., Xia, D., Dai, J.-B., Wu, H., Choi, H.-K. & Lynch, R. E. (1992). Molecular replacement real-space averaging. J. Appl. Cryst. 25, 166–180.Google Scholar
Sack, J. S. (1988). CHAIN – a crystallographic modeling program. J. Mol. Graphics, 6, 224–225.Google Scholar
Schuller, D. J. (1996). MAGICSQUASH: more versatile non-crystallographic averaging with multiple constraints. Acta Cryst. D52, 425–434.Google Scholar
Sheldrick, G. M. (1985). Computing aspects of crystal structure determination. J. Mol. Struct. 130, 9–16.Google Scholar
Sheldrick, G. M. (1990). Phase annealing in SHELX-90: direct methods for larger structures. Acta Cryst. A46, 467–473.Google Scholar
Sheldrick, G. M. (1991). Tutorial on automated Patterson interpretation to find heavy atoms. In Crystallographic computing 5. From chemistry to biology, edited by D. Moras, A. D. Podjarny & J. C. Thierry, pp. 145–157. Oxford: IUCr and Oxford University Press.Google Scholar
Sheldrick, G. M. (1993). Refinement of large small-molecule structures using SHELXL-92. In Crystallographic computing 6. A window on modern crystallography, edited by H. D. Flack, L. Párkányi & K. Simon, pp. 111–122. Oxford: IUCr and Oxford University Press.Google Scholar
Sheldrick, G. M. (1997). Direct methods based on real/reciprocal space iteration. In Proceedings of the CCP4 study weekend. Recent advances in phasing, edited by K. S. Wilson, G. Davies, A. W. Ashton & S. Bailey, pp. 147–157. Warrington: Daresbury Laboratory.Google Scholar
Sheldrick, G. M. (1998a). Location of heavy atoms by automated Patterson interpretation. In Direct methods for solving macromolecular structures, edited by S. Fortier, pp. 131–141. Dordrecht: Kluwer Academic Publishers.Google Scholar
Sheldrick, G. M. (1998b). SHELX: applications to macromolecules. In Direct methods for solving macromolecular structures, edited by S. Fortier, pp. 401–411. Dordrecht: Kluwer Academic Publishers.Google Scholar
Sheldrick, G. M., Dauter, Z., Wilson, K. S., Hope, H. & Sieker, L. C. (1993). The application of direct methods and Patterson interpretation to high-resolution native protein data. Acta Cryst. D49, 18–23.Google Scholar
Sheldrick, G. M. & Gould, R. O. (1995). Structure solution by iterative peaklist optimization and tangent expansion in space group P1. Acta Cryst. B51, 423–431.Google Scholar
Sheldrick, G. M. & Schneider, T. R. (1997). SHELXL: high resolution refinement. Methods Enzymol. 277, 319–343.Google Scholar
Sim, G. A. (1959). The distribution of phase angles for structures containing heavy atoms. II. A modification of the normal heavy-atom method for non-centrosymmetrical structures. Acta Cryst. 12, 813–814.Google Scholar
Stout, G. H. & Jensen, L. H. (1989). X-ray structure determination, p. 33. New York: Wiley Interscience.Google Scholar
Sussman, J. L., Holbrook, S. R., Church, G. M. & Kim, S.-H. (1977). A structure-factor least-squares refinement procedure for macromolecular structures using constrained and restrained parameters. Acta Cryst. A33, 800–804.Google Scholar
Ten Eyck, L. F. (1973). Crystallographic fast Fourier transforms. Acta Cryst. A29, 183–191.Google Scholar
Ten Eyck, L. F. (1977). Efficient structure-factor calculation for large molecules by the fast Fourier transform. Acta Cryst. A33, 486–492.Google Scholar
Terwilliger, T. C. & Berendzen, J. (1996). Bayesian weighting for macromolecular crystallographic refinement. Acta Cryst. D52, 743–748.Google Scholar
Terwilliger, T. C. & Eisenberg, D. (1987a). Isomorphous replacement: effects of errors on the phase probability distribution. Acta Cryst. A43, 6–13.Google Scholar
Terwilliger, T. C. & Eisenberg, D. (1987b). Isomorphous replacement: effects of errors on the phase probability distribution. Erratum. Acta Cryst. A43, 286.Google Scholar
Tickle, I. J., Laskowski, R. A. & Moss, D. S. (1998). Error estimates of protein structure coordinates and deviations from standard geometry by full-matrix refinement of γB- and γB2-crystallin. Acta Cryst. D54, 243–252.Google Scholar
Tronrud, D. E. (1992). Conjugate-direction minimization: an improved method for the refinement of macromolecules. Acta Cryst. A48, 912–916.Google Scholar
Tronrud, D. E. (1996). Knowledge-based B-factor restraints for the refinement of proteins. J. Appl Cryst. 29, 100–104.Google Scholar
Tronrud, D. E. (1997). TNT refinement package. Methods Enzymol. 277, 306–319.Google Scholar
Tronrud, D. E., Ten Eyck, L. F. & Matthews, B. W. (1987). An efficient general-purpose least-squares refinement program for macromolecular structures. Acta Cryst. A43, 489–501.Google Scholar
Trueblood, K. N. & Dunitz, J. D. (1983). Internal molecular motions in crystals. The estimation of force constants, frequencies and barriers from diffraction data. A feasibility study. Acta Cryst. B39, 120–133.Google Scholar
Tsao, J., Chapman, M. S. & Rossmann, M. G. (1992). Ab initio phase determination for viruses with high symmetry: a feasibility study. Acta Cryst. A48, 293–301.Google Scholar
Usón, I., Pohl, E., Schneider, T. R., Dauter, Z., Schmidt, A., Fritz, H.-J. & Sheldrick, G. M. (1999). 1.7 Å structure of the stabilised RE!v mutant T39K. Application of local NCS restraints. Acta Cryst. D55, 1158–1167.Google Scholar
Vellieux, F. M. D. A. P., Hunt, J. F., Roy, S. & Read, R. J. (1995). DEMON/ANGEL: a suite of programs to carry out density modification. J. Appl. Cryst. 28, 347–351.Google Scholar
Walther, D. & Cohen, F. E. (1999). Conformational attractors on the Ramachandran map. Acta Cryst. D55, 506–517.Google Scholar
Wang, B. C. (1985). Resolution of phase ambiguity in macromolecular crystallography. Methods Enzymol. 115, 90–112.Google Scholar
Watenpaugh, K. D., Sieker, L. C., Herriott, J. R. & Jensen, L. H. (1973). Refinement of the model of a protein: rubredoxin at 1.5 Å resolution. Acta Cryst. B29, 943–956.Google Scholar
Weis, W. I., Brünger, A. T., Skehel, J. J. & Wiley, D. C. (1990). Refinement of the influenza virus haemagglutinin by simulated annealing. J. Mol. Biol. 212, 737–761.Google Scholar
Wilson, A. J. C. (1949). The probability distribution of X-ray intensities. Acta Cryst. 2, 318–321.Google Scholar
Wilson, K. S., Butterworth, S., Dauter, Z., Lamzin, V. S., Walsh, M., Wodak, S., Pontius, J., Richelle, J., Vaguine, A., Sander, C., Hooft, R. W. W., Vriend, G., Thornton, J. M., Laskowski, R. A., MacArthur, M. W., Dodson, E. J., Murshudov, G., Oldfield, T. J., Kaptein, R. & Rullmann, J. A. C. (1998). Who checks the checkers? Four validation tools applied to eight atomic resolution structures. J. Mol. Biol. 276, 417–436.Google Scholar
Word, J. M., Bateman, R. C., Presley, B. K., Lovell, S. C. & Richardson, D. C. (2000). Exploring steric constraints on protein mutations using MAGE/PROBE. Protein Sci. 11, 2251–2259.Google Scholar
Word, J. M., Lovell, S. C., LaBean, T. H., Taylor, H. C., Zalis, M. E., Presley, B. K., Richardson, J. S. & Richardson, D. C. (1999). Visualizing and quantifying molecular goodness-of-fit: small-probe contact dots with explicit hydrogen atoms. J. Mol. Biol. 285, 1711–1733.Google Scholar
Word, J. M., Lovell, S. C., Richardson, J. S. & Richardson, D. C. (1999). Asparagine and glutamine: using hydrogen atom contacts in the choice of side-chain amide orientation. J. Mol. Biol. 285, 1735–1747.Google Scholar
Yeates, T. O. & Fam, B. C. (1999). Protein crystals and their evil twins. Structure, 7, R25–R29.Google Scholar
Zhang, K. Y. J. & Main, P. (1990a). Histogram matching as a new density modification technique for phase refinement and extension of protein molecules. Acta Cryst. A46, 41–46.Google Scholar
Zhang, K. Y. J. & Main, P. (1990b). The use of Sayre's equation with solvent flattening and histogram matching for phase extension and refinement of protein structures. Acta Cryst. A46, 377–381.Google Scholar